High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol

Area of Science:

• Genomics
• Virology
• Bioinformatics

Background:

• The COVID-19 pandemic necessitated rapid genomic surveillance of SARS-CoV-2.
• High-throughput sequencing is crucial for tracking viral evolution and emergence of variants.

Purpose of the Study:

• To develop and validate a rapid, cost-effective sequencing protocol for 384 SARS-CoV-2 samples.
• To adapt Illumina NovaSeq libraries for use on an Illumina MiSeq instrument.

Main Methods:

• A modified Illumina COVIDSeq protocol was developed by adapting NovaSeq library preparation for MiSeq instruments.
• The modified protocol was used to sequence 384 samples, and results were compared to the standard COVIDSeq protocol.
• Sequence data quality and coverage were analyzed for both protocols.

Main Results:

• The modified protocol yielded interpretable sequences for 94.6% of samples with 91.6% average coverage.
• The standard protocol yielded interpretable sequences for 94.9% of samples with 95.6% average coverage.
• The modified protocol reduced run time to 53.5 hours and saved 14,155 euros per run compared to the standard protocol.

Conclusions:

• The modified COVIDSeq protocol offers a rapid, cost-effective alternative for SARS-CoV-2 genome sequencing.
• This protocol provides high-quality results comparable to the standard method, enabling faster viral surveillance.
• The adapted protocol significantly improves efficiency for large-scale sequencing efforts during pandemics.